Where I reported yesterday the initial steps of an client R package for Open PHACTS, I can now report the first pharmacology data import:

Nothing much going to say about it, and just to report some progress:

Short post, but with big implications. John released CDK 1.5.4 which mostly consists of great work on his side on various important corners of the CDK. Make sure to read his blog, and some highlights:

New SMILES behaviour - parsing Improved Substructure Matching AllRingsFinder, Sport Edition Everyone who is still using a version from the CDK 1.4 series, should really consider switching over (just read the 1.5.2, 1.5.3, and 1.5.4 changelogs for the reason why).

Hot on the heels of the announcement that the Open PHACTS LDA was hit over 8M times, here are some usage statistics of the Programming in the Life Sciences course. Basically consisting of six practical days (with expected reading at home), we see a spiked pattern:

You can always hope that students continue their work at home, and some do:

And some students wait until the very end with finishing their work:

Thanks for Paul Groth for suggesting 3scale.net.

After five earlier screenshots, here follow a sixth one. That sums up all the projects I have received at this moment for Programming in the Life Science course. The team of Sam and Oskar decided to use a tree layout to show the pathways in which a selected compound is found, and a subset of targets and compounds for that pathway.

Ever since I upgraded to Virtuoso OS 7.0 I have had trouble keeping the SPARQL endpoint at Uppsala University for the ChEMBL-RDF v13 data online (see doi:10.1186/1758-2946-5-23; ChEMBL is CC-BY-SA by the Overington team). It seems I am not getting all the settings right, or not as right as for VOS6 which ran for more than two years without the same downtime issues.

Two more projects were handed in for Programming in the Life Sciences late last night (see also the first three).

I got a one more source code zip file from the Maastricht Science Programme students (see also the first two screenshots).

Yesterday was the last Programming in the Life Sciences practical day, and the 2nd and 3rd year B.Sc. MSC students presented their results yesterday afternoon. I am impressed with the results that they reached in only six practical days. I have suggested them to upload the presentations to SlideShare or FigShare (with the advantage that you get a DOI), and asked them to send them their tools. Below are some screenshots.
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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